Compounding Achromobacter Phages for Therapeutic Applications

<i>Achromobacter</i> species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by <i>Achromobacter xylosoxidans</i> CF418 or <i>Achromobacter ruhlandii</i> CF116 experienced fatal exacerbations. <i>Achromobacter</i> spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of <i>Achromobacter</i>. In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the <i>Achromobacter</i> Kumeyaay phage collection. Six distinct <i>Achromobacter</i> phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available <i>Achromobacter</i> phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 <i>Achromobacter</i> clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in <i>Achromobacter xylosoxidans</i> CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as <i>Achromobacter</i> phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 × 10⁹ plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill <i>Achromobacter</i> spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.